Function wrappers, new package data, new vignettes (#32)

* Function wrappers, new package data, new vignettes

* More merge changes

.gitignore

@@ -22,6 +22,7 @@
 /*.Rcheck/
 
 # RStudio files
+*.Rproj
 .Rproj.user/
 
 # produced vignettes

DESCRIPTION

@@ -11,16 +11,23 @@ License: MIT + file LICENSE
 Suggests: 
     dplyr,
     ggplot2,
+    ggpubr,
+    httk,
     knitr,
+    readr,
+    readxl,
     rmarkdown,
     scales,
+    sf,
+    stringr,
     testthat (>= 3.0.0),
     tidyr
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Imports: 
+    methods,
     truncnorm
 VignetteBuilder: knitr
 Depends: 

NAMESPACE

@@ -3,8 +3,9 @@
 export(calc_concentration_response)
 export(calc_internal_dose)
 export(calc_invitro_concentration)
-export(extract_hill_params)
 export(fit_hill)
+export(sample_Css)
 export(simulate_age)
 export(simulate_exposure)
 export(simulate_inhalation_rate)
+export(simulate_obesity)

R/calc_concentration_response.R

@@ -1,54 +1,70 @@
 #' Calculate the mixture response from one of three different approaches:
 #' IA, GCA ,or Hazard Quotient
 #'
-#' @param resp data frame with columns "tp", "tp.sd", "logAC50", "logAC50.sd",
-#' "resp_max", "logc_min", "logc_max".
-#' @param concentration concentration
+#' @param C_invitro in vitro concentrations
+#' @param hill_params output from `fit_hill()`
 #' @param tp_b_mult upper bound multiplier for tp rtruncnorm
 #' @param fixed if TRUE, sd = 0
 #'
 #' @description
 #' Calculate the combined response of multiple chemicals. It calculates the
 #' generalized concentration addition response, the independent action
 #' response, and a hazard quotient
+#'
 #' @return data frame
+#'
 #' @export
 calc_concentration_response <- function(
-    resp, concentration, tp_b_mult = 1.5, fixed = FALSE
+    C_invitro, hill_params, tp_b_mult = 1.5, fixed = FALSE
 ) {
 
-  # TODO make inputs more general
-  # TODO add input for linear/log concentration
-  # TODO maybe add option for ln(resp) or not
+  if (methods::is(C_invitro, "matrix")) {
+    .calc_concentration_response(C_invitro, hill_params, tp_b_mult, fixed)
+  } else {
+    mapply(
+      .calc_concentration_response,
+      C_invitro = C_invitro,
+      hill_params = list(hill_params),
+      tp_b_mult = tp_b_mult,
+      fixed = fixed,
+      SIMPLIFY = FALSE
+    )
+  }
+
+}
+
+.calc_concentration_response <- function(
+    C_invitro, hill_params, tp_b_mult, fixed
+) {
 
   interval <- c(-50,50)
 
   # TODO value of b not consistent
   # grep "tp.sim <-" ~/github/GeoToxMIE/*.R
-  tp <- t(sapply(1:nrow(concentration), function(x) {
+  tp <- t(sapply(1:nrow(C_invitro), function(x) {
     truncnorm::rtruncnorm(
       1,
       a    = 0,
-      b    = resp$resp_max * tp_b_mult,
-      mean = resp$tp,
-      sd   = if (fixed) 0 else resp$tp.sd
+      b    = hill_params$resp_max * tp_b_mult,
+      mean = hill_params$tp,
+      sd   = if (fixed) 0 else hill_params$tp.sd
     )
   }))
 
-  logAC50 <- t(sapply(1:nrow(concentration), function(x) {
+  logAC50 <- t(sapply(1:nrow(C_invitro), function(x) {
     truncnorm::rtruncnorm(
       1,
-      a    = resp$logc_min - 2,
-      b    = resp$logc_max + 0.5,
-      mean = resp$logAC50,
-      sd   = if (fixed) 0 else resp$logAC50.sd
+      a    = hill_params$logc_min - 2,
+      b    = hill_params$logc_max + 0.5,
+      mean = hill_params$logAC50,
+      sd   = if (fixed) 0 else hill_params$logAC50.sd
     )
   }))
 
-  GCA.eff <- IA.eff <- GCA.HQ.10  <- IA.HQ.10 <- rep(NA, nrow(concentration))
-  for (i in 1:nrow(concentration)) {
+  GCA.eff <- IA.eff <- GCA.HQ.10 <- IA.HQ.10 <- rep(NA, nrow(C_invitro))
+  for (i in 1:nrow(C_invitro)) {
 
-    C_i <- concentration[i, ]
+    C_i <- C_invitro[i, ]
     tp_i <- tp[i, ]
     AC50_i <- 10^logAC50[i, ]
 

R/calc_internal_dose.R

@@ -1,24 +1,53 @@
 #' Calculate internal chemical dose
 #'
 #' @description
-#' Estimate the internal dose from inhalation of a chemical given inhalation rate, time, and body weight
+#' Estimate the internal dose from inhalation of a chemical given inhalation
+#' rate, time, and body weight
 #'
 #' @param C_ext ambient chemical concentration in \eqn{\frac{mg}{m^3}}
 #' @param IR inhalation rate in \eqn{\frac{m^3}{day}}
 #' @param time total time in \eqn{days}
 #' @param BW body weight in \eqn{kg}
+#' @param scaling scaling factor encompassing any required unit adjustments
 #'
 #' @details
 #' TODO Additional details...
 #' \deqn{D_{int} = \frac{C_{ext} \,\times\, IR \,\times\, time}{BW}}
 #'
 #' @return internal chemical dose in \eqn{\frac{mg}{kg}}
+#'
+#' @examples
+#' n_chem <- 3
+#' n_sample <- 5
+#'
+#' # Single population
+#' C_ext <- matrix(runif(n_sample * n_chem), ncol = n_chem)
+#' IR <- runif(n_sample)
+#' calc_internal_dose(C_ext, IR)
+#'
+#' # Multiple populations
+#' C_ext <- list(
+#'   "a" = matrix(runif(n_sample * n_chem), ncol = n_chem),
+#'   "b" = matrix(runif(n_sample * n_chem), ncol = n_chem)
+#' )
+#' IR <- list(runif(n_sample), runif(n_sample))
+#' calc_internal_dose(C_ext, IR)
+#'
 #' @export
-calc_internal_dose <- function(C_ext, IR, time = 1, BW = 1) {
+calc_internal_dose <- function(C_ext, IR, time = 1, BW = 1, scaling = 1) {
   # TODO How to handle inputs with different units?
   # e.g. simulated inhalation rate is in m^3/(day * kg), so BW isn't needed
   # TODO paper states t = 365 in section 2.3, also states that C_ss achieved
   # in 1 day and repeated exposure accumulates additively. Computation done
   # with t = 1, is that correct?
-  C_ext * IR * time / BW
+
+  if (methods::is(C_ext, "matrix")) {
+    .calc_internal_dose(C_ext, IR, time, BW, scaling)
+  } else {
+    mapply(.calc_internal_dose, C_ext, IR, time, BW, scaling, SIMPLIFY = FALSE)
+  }
+}
+
+.calc_internal_dose <- function(C_ext, IR, time, BW, scaling) {
+  C_ext * IR * time / BW * scaling
 }

R/calc_invitro_concentration.R

@@ -10,16 +10,25 @@
 #' TODO Additional details...
 #' \deqn{C_{plasma} = C_{ss} \,\times\, D_{int}}
 #'
-#' TODO If C_ss is not provided, uses \emph{httk} to create...
-#'
 #' @return \emph{in vitro} equivalent plasma concentration in \eqn{\mu M}
 #' @export
 calc_invitro_concentration <- function(D_int, C_ss = NULL) {
+
   if (is.null(C_ss)) {
     # TODO add real-time computation of Css values
     stop("real-time computation of Css values has not been implemented")
   }
+
   # TODO the current C_ss data passed into this for step 01-Sensitivity.R
   # doesn't match the ages that were simulated?
+
+  if (methods::is(D_int, "matrix")) {
+    .calc_invitro_concentration(D_int, C_ss)
+  } else {
+    mapply(.calc_invitro_concentration, D_int, C_ss, SIMPLIFY = FALSE)
+  }
+}
+
+.calc_invitro_concentration <- function(D_int, C_ss) {
   D_int * C_ss
 }

R/data.R

@@ -1,21 +1,19 @@
 #' Geo Tox data
 #'
-#' A subset of data from the GeoToxMIE source scripts
+#' Sample data for use in vignettes and function examples. See the
+#' "package_data" vignette for details on how this data was gathered.
 #'
-#' @format A list with 4 items:
+#' @format A list with items:
 #' \describe{
-#'   \item{ice}{Description}
-#'   \item{MC_iter}{Description}
-#'   \item{cyp1a1}{Description}
-#'   \item{age}{Description}
-#'   \item{Css}{Description}
-#' }
-#' Css is a list with 5 items:
-#' \describe{
-#'   \item{Css$age}{Description}
-#'   \item{Css$obesity}{Description}
-#'   \item{Css$httk}{Description}
-#'   \item{Css$'dose-resp'}{Description}
-#'   \item{Css$'ext-conc'}{Description}
+#'   \item{exposure}{2019 AirToxScreen exposure concentrations for a subset of
+#'   chemicals in North Carolina counties}
+#'   \item{dose_response}{A subset of data from InvitroDB for the
+#'   "LTEA_HepaRG_CYP1A1_up" assay}
+#'   \item{age}{County population estimates for 7/1/2019 in North Carolina}
+#'   \item{obesity}{CDC PLACES obesity data for North Carolina counties in
+#'   2020}
+#'   \item{simulated_css}{Simulated steady-state plasma concentrations for
+#'   various age groups and obesity status combinations}
+#'   \item{boundaries}{County and state boundaries for North Carolina in 2019}
 #' }
 "geo_tox_data"